psSubpathway (version 0.1.3)

plotheatmap: Plot a heatmap

Description

Plot a heatmap of subpathway activity profile based on the parameters set by the user.

Usage

plotheatmap(
  inputdata,
  plotSubSEA = TRUE,
  fdr.th = 1,
  SES = "positive",
  phenotype = "all"
)

Value

a heatmap

Arguments

inputdata

A list of result data generated by function `SubSEA` or `DCSA`.

plotSubSEA

Determine the inputdata is the result data of function `SubSEA` (default:plotSubSEA=TRUE) or `DCSA` (plotSubSEA=FLASE).

fdr.th

Cutoff value for FDR. The only subpathway with lower FDR is plotted. (default: 1).

SES

Parameter `SES` is useful only when `plotSubSEA` is TRUE. When `plotSubSEA=TRUE`,if `SES` is positive, the subpathway with high-expression will be plotted. when it is negative, plot low-expression subpathways.

phenotype

Parameter `phenotype` is useful only when `plotSubSEA` is TRUE. `phenotype` decides which phenotypic significant subpathways to screen (which phenotypic result is applied to parameter `fdr.th` and `SES`.) and plot a heat map of these subpathways.By default,`phenotype="all"` which will screen the subpathways of all phenotypes and plot a heat map. When the user wants to plot a subpathway heat map of the specified phenotype, this parameter should be set to the name of the phenotype.

Author

Xudong Han, Junwei Han, Qingfei Kong

Details

plotheatmap

The subpathways are screened according to the conditions set by the user and a heat map of the activity of these subpathways is drawn.

Examples

# load depend package.
library(pheatmap)
# get the Subspwresult which is the result of SubSEA function.
Subspwresult<-get("Subspwresult")
# get the DCspwresult which is the result of DCSA function.
DCspwresult<-get("DCspwresult")
# plot significant up-regulation subpathway heat map specific for each breast cancer subtype.
plotheatmap(Subspwresult,plotSubSEA=TRUE,fdr.th=0.01,SES="positive",phenotype="all")
# plot significant down-regulation subpathway heat map specific for each breast cancer subtype.
plotheatmap(Subspwresult,plotSubSEA=TRUE,fdr.th=0.01,SES="negative",phenotype="all")
# plot basal subtype specific significant subpathway heat map.
plotheatmap(Subspwresult,plotSubSEA=TRUE,fdr.th=0.01,SES="all",phenotype="Basal")
# plot adrenocortical cancer disease stages specific significant subpathway heat map.
plotheatmap(DCspwresult,plotSubSEA=FALSE,fdr.th=0.01)